1EON | pdb_00001eon

ECORV BOUND TO 3'-S-PHOSPHOROTHIOLATE DNA AND CA2+

• PDB DOI: https://doi.org/10.2210/pdb1EON/pdb
• NAKB: 1EON

• Classification: hydrolase/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-03-23 Released: 2000-04-04 
• Deposition Author(s): Horton, N.C., Connolly, B.A., Perona, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.281 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study

Horton, N.C., Connolly, B.A., Perona, J.J.

(2000) J Am Chem Soc 122: 3314-3324

• DOI: https://doi.org/10.1021/ja993719j

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.36 kDa 
• Atom Count: 4,587 
• Modeled Residue Count: 492 
• Deposited Residue Count: 512 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE II RESTRICTION ENZYME ECORV	C [auth A], D [auth B]	245	Escherichia coli	Mutation(s): 0  EC: 3.1.21.4
UniProt
Find proteins for P04390 (Escherichia coli) Explore P04390  Go to UniProtKB:  P04390

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')	A [auth C]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')	B [auth D]	11	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	G [auth A], J [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.281 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.9	α = 96.9
b = 48.6	β = 108.9
c = 63.9	γ = 106.8

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-04 
Deposition Author(s): Horton, N.C., Connolly, B.A., Perona, J.J.

Revision History  

• Version 1.0: 2000-04-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-31
  Changes: Data collection, Derived calculations
• Version 2.0: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Polymer sequence